Judging on general grounds, I would say including correction terms for van der Waals interaction makes sense when doing geometry optimization of a van der Waals system. The obtained structure can then be used to build a device configuration with no van der Waals terms included, since they would have a minor or perhaps no effect on the electron transmission, as they do not cause any hybridization of states.
So, it is very likely that the authors mean structural relaxation done with van der Waals corrections, but not the actual device calculations to get conductance or current for a fixed device structure.